Wright S. Evolution in Mendelian populations. Genetics. 1931; 16:97–159.

CAS
PubMed
PubMed Central
Google Scholar

Pigliucci M. Sewall Wright’s adaptive landscapes: 1932 vs. 1988. Biol Philos. 2008; 23:591–603.

Article
Google Scholar

Svensson EI, Calsbeek R. The Adaptive Landscape in Evolutionary Biology. Oxford: Oxford University Press; 2012.

Google Scholar

Wright S. The roles of mutation, inbreeding, crossbreeding and selection in evolution. Proc 6 ^{th} Int Congr Genet. 1932; 1:356–66.

Google Scholar

Mustonen V, Lässig M. From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation. Trends Genet. 2009; 25:111–9.

Article
CAS
PubMed
Google Scholar

Gavrilets S. Fitness Landscapes and the Origin of Species. Princeton: Princeton University Press; 2004.

Google Scholar

Pigliucci M. Landscapes, surfaces, and morphospaces: what are they good for? In: Svensson E, Calsbeek R, (eds.), editors. The Adaptive Landscape in Evolutionary Biology. Oxford: Oxford University Press: 2012. p. 26–38. Chap. 3.

Smith JM. Natural selection and the concept of a protein space. Nature. 1970; 225:563–4.

Article
CAS
PubMed
Google Scholar

Huynen MA, Stadler PF, Fontana W. Smoothness within ruggedness: The role of neutrality in adaptation. Proc Natl Acad Sci USA. 1996; 93:397–401.

Article
CAS
PubMed
PubMed Central
Google Scholar

Bastolla U, Porto M, Roman HE, Vendruscolo M. Connectivity of neutral networks, overdispersion, and structural conservation in protein evolution. J Mol Evol. 2003; 56:243–54.

Article
CAS
PubMed
Google Scholar

Ciliberti S, Martin OC, Wagner A. Innovation and robustness in complex regulatory gene networks. Proc Natl Acad Sci USA. 2007; 104:13591–6.

Article
CAS
PubMed
PubMed Central
Google Scholar

Rodrigues JFM, Wagner A. Genotype networks, innovation, and robustness in sulfur metabolism. BMC Syst Biol. 2011; 5:39.

Article
CAS
Google Scholar

Schultes EA, Bartel DP. One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science. 2000; 289:448–52.

Article
CAS
PubMed
Google Scholar

Bloom JD, Romero PA, Lu Z, Arnold FH. Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution. Biol Dir. 2007; 2:17.

Article
Google Scholar

Koelle K, Cobey S, Grenfell B, Pascual M. Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans. Science. 2006; 314:1898–903.

Article
CAS
PubMed
Google Scholar

Gavrilets S. Evolution and speciation on holey adaptive landscapes. Trends Ecol Evol. 1997; 12:307–12.

Article
CAS
PubMed
Google Scholar

Kaplan J. The end of the adaptive landscape metaphor?Biol Philos. 2008; 23:625–38.

Article
Google Scholar

Gould SJ, Vrba ES. Exaptation – a missing term in the science of form. Paleobiology. 1982; 8:4–15.

Article
Google Scholar

Conant GC, Wolfe KH. Turning a hobby into a job: How duplicated genes find new functions. Nat Rev Genet. 2008; 9:938–50.

Article
CAS
PubMed
Google Scholar

Gavrilets S, Gravner J. Percolation on the fitness hypercube and the evolution of reproductive isolation. J Theor Biol. 1997; 184:51–64.

Article
CAS
PubMed
Google Scholar

Huynen MA. Exploring phenotype space through neutral evolution. J Mol Evol. 1996; 43:165–9.

Article
CAS
PubMed
Google Scholar

Babajide A, Hofacker IL, Sippl MJ, Stadler PF. Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force. Fold Des. 1997; 2:261–9.

Article
CAS
PubMed
Google Scholar

Eyre-Walker A, Keightley PD. The distribution of fitness effects of new mutations. Nat Revs Genet. 2007; 8:610–8.

Article
CAS
Google Scholar

Grüner W, Giegerich R, Strothmann D, Reidys C, Weber J, Hofacker IL, Stadler PF, Schuster P. Analysis of RNA sequence structure maps by exhaustive enumeration. I. Neutral networks. Monatsh Chem. 1996; 127:355–74.

Article
Google Scholar

Cowperthwaite MC, Economo EP, Harcombe WR, Miller EL, Meyers LA. The ascent of the abundant: How mutational networks constrain evolution. PLoS Comp Biol. 2008; 4:1000110.

Article
Google Scholar

Dingle K, Schaper S, Louis AA. The structure of the genotype-phenotype map strongly constrains the evolution of non-coding RNA. J R Soc Interf Focus. 2015; 5:20150053.

Article
Google Scholar

Irbäck A, Troein C. Enumerating designing sequences in the HP model. J Biol Phys. 2002; 28:1–15.

Article
PubMed
PubMed Central
Google Scholar

Holzgräfe C, Irbäck A, Troein C. Mutation-induced forld switching among lattice proteins. J Chem Phys. 2011; 135:195101.

Article
PubMed
Google Scholar

Jörg T, Martin OC, Wagner A. Neutral network sizes of biological RNA molecules can be computed and are not atypically small. BMC Bioinforma. 2008; 9:464.

Article
Google Scholar

Stich M, Briones C, Manrubia SC. On the structural repertoire of pools of short, random RNA sequences. J Theor Biol. 2008; 252:750–63.

Article
CAS
PubMed
Google Scholar

Schuster P, Fontana W, Stadler PF, Hofacker IL. From sequences to shapes and back: a case study in RNA secondary structures. Proc R Soc Lond B. 1994; 255:279–84.

Article
CAS
Google Scholar

Aguirre J, Buldú JM, Stich M, Manrubia SC. Topological structure of the space of phenotypes: The case of RNA secondary structure. PLoS ONE. 2011; 6:26324.

Article
Google Scholar

Greenbury SF, Ahnert SE. The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype–phenotype maps. J Royal Soc Interface. 2015; 12:20150724.

Article
CAS
Google Scholar

Wilke CO, Wang JL, Ofria C, Lenski RE, Adami C. Evolution of digital organisms at high mutation rates leads to survival of the flattest. Nature. 2001; 412:331–3.

Article
CAS
PubMed
Google Scholar

Codoñer FM, Darós JA, Solé RV, Elena SF. The fittest versus the flattest: Experimental confirmation of the quasispecies effect with subviral pathogens. PLoS Path. 2006; 2:136.

Article
Google Scholar

Bornberg-Bauer E. How are model protein structures distributed in sequence space?. Biophys J. 1997; 73:2393–403.

Article
CAS
PubMed
PubMed Central
Google Scholar

Johnston IG, Ahnert SE, Doye JPK, Louis AA. Evolutionary dynamics in a simple model of self-assembly. Phys Rev E. 2011; 83:066105.

Article
Google Scholar

Wagner A. The Origins of Evolutionary Innovations. New York: Oxford University Press; 2011.

Book
Google Scholar

Lynch M. The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci USA. 2007; 104:8597–604.

Article
CAS
PubMed
PubMed Central
Google Scholar

Fontana W, Schuster P. Continuity in evolution: On the nature of transitions. Science. 1998; 280:1451–5.

Article
CAS
PubMed
Google Scholar

Fontana W, Schuster P. Shaping space: the possible and the attainable in RNA genotype-phenotype mapping. J Theor Biol. 1998; 194:491–515.

Article
CAS
PubMed
Google Scholar

Fontana W. Modelling ’evo-devo’ with RNA. BioEssays. 2002; 24:1164–77.

Article
CAS
PubMed
Google Scholar

Schaper S, Louis AA. The arrival of the frequent: How bias in genotype-phenotype maps can steer populations to local optima. PLoS ONE. 2014; 9:86635.

Article
Google Scholar

McCaskill J. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers. 1990; 29:1105–19.

Article
CAS
PubMed
Google Scholar

García-Martín JA, Bayegan AH, Dotu I, Clote P. Rnadualpf: software to compute the dual partition function with sample applications in molecular evolution theory. BMC Bioinforma. 2016; 17:424.

Article
Google Scholar

Reidys C, Stadler PF, Schuster P. Generic properties of combinatory maps: neutral networks of RNA secondary structures. Bull Math Biol. 1997; 59:339–97.

Article
CAS
PubMed
Google Scholar

Manzourolajdad A, Arnold J. Secondary structural entropy in RNA switch (riboswitch) identification. BMC Bioinforma. 2015; 16:133.

Article
Google Scholar

Vaidya N, Lehman N. One RNA plays three roles to provide catalytic activity to a group I intron lacking an endogenous internal guide sequence. Nucl Acids Res. 2009; 37:3981–9.

Article
CAS
PubMed
PubMed Central
Google Scholar

Piatigorsky J. Gene Sharing and Evolution: the Diversity of Protein Functions. Cambridge: Harvard University Press; 2007.

Book
Google Scholar

Wistow G, Piatigorsky J. Recruitment of enzymes as lens structural proteins. Science. 1987; 236:1554–6.

Article
CAS
PubMed
Google Scholar

Jensen RA. Enzyme recruitment in evolution of new function. Annu Rev Microbiol. 1976; 30:409–25.

Article
CAS
PubMed
Google Scholar

Aharoni A, Gaidukov L, Khersonsky O, Gould SM, Roodveldt C, Tawfik DS. The “evolvability” of promiscuous protein functions. Nat Gen. 2005; 37:73.

CAS
Google Scholar

Barve A, Wagner A. A latent capacity for evolutionary innovation through exaptation in metabolic systems. Nature. 2013; 500:203–8.

Article
CAS
PubMed
Google Scholar

Arias CF, Catalán P, Manrubia S, Cuesta JA. toyLIFE: a computational framework to study the multi-level organization of the genotype-phenotype map. Sci Rep. 2014; 4:7549.

Article
CAS
PubMed
PubMed Central
Google Scholar

Amitai G, Gupta RD, Tawfik DS. Latent evolutionary potentials under the neutral mutational drift of an enzyme. HFSP J. 2007; 1:67–78.

Article
CAS
PubMed
PubMed Central
Google Scholar

Aguirre J, Buldú JM, Manrubia SC. Evolutionary dynamics on networks of selectively neutral genotypes: Effects of topology and sequence stability. Phys Rev E. 2009; 80:066112.

Article
Google Scholar

Wagner A. Robustness and evolvability: A paradox resolved. Proc Roy Soc Lond B. 2008; 275:91–100.

Article
Google Scholar

Manrubia S, Cuesta JA. Evolution on neutral networks accelerates the ticking rate of the molecular clock. J R Soc Interf. 2015; 12:20141010.

Article
Google Scholar

Duarte EA, Novella IS, Ledesma S, Clarke DK, Moya A, Elena SF, Domingo E, Holland JJ. Subclonal components of consensus fitness in an RNA virus clone. J Virol. 1994; 68:4295–301.

CAS
PubMed
PubMed Central
Google Scholar

Manrubia S, Lázaro E, Pérez-Mercader J, Escarmís C, Domingo E. Fitness distribution in exponentially growing asexual populations. Phys Rev Lett. 2003; 90:188102.

Article
PubMed
Google Scholar

Lafforgue G, Martínez F, Sardanyés J, de la Iglesia F, Niu QW, Lin SS, Solé RV, Chua NH, Daròs JA, Elena SF. Tempo and mode of plant RNA Virus Escape from RNA interference-mediated resistance. J Virol. 2011; 85:9686.

Article
CAS
PubMed
PubMed Central
Google Scholar

Coffin JM. HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy. Science. 1995; 267:483–9.

Article
CAS
PubMed
Google Scholar

Alexander HK, Bonhoeffer S. Pre-existence and emergence of drug resistance in a generalized model of intra-host viral dynamics. Epidemics. 2012; 4:187–202.

Article
PubMed
Google Scholar

Innan H, Kondrashov F. The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet. 2010; 11:97–108.

Article
CAS
PubMed
Google Scholar

Waddington CH. Genetic assimilation of an acquired character. Evolution. 1953; 7:118–26.

Article
Google Scholar

Waddington CH. Genetic assimilation of the *bithorax* phenotype. Evolution. 1956; 10:1–13.

Article
Google Scholar

Schenk MF, Szendro IG, Salverda MLM, Krug J, de Visser JAGM. Patterns of epistasis between beneficial mutations in an antibiotic resistance gene. Mol Biol Evol. 2013; 30:1779–87.

Article
CAS
PubMed
PubMed Central
Google Scholar

Whitehead DJ, Wilke CO, Vernazobres D, Bornberg-Bauer E. The look-ahead effect of phenotypic mutations. Biol Direct. 2008; 3:18.

Article
PubMed
PubMed Central
Google Scholar

Ancel LW, Fontana W. Plasticity, evolvability, and modularity in rna. J Exp Zool. 2000; 288:242–83.

Article
CAS
PubMed
Google Scholar

Borenstein E, Meilijson I, Ruppin E. The effect of phenotypic plasticity on evolution in multipeaked fitness landscapes. J Evol Biol. 2006; 19:1555–70.

Article
CAS
PubMed
Google Scholar

Kin T, Yamada K, Terai G, Okida H, Yoshinari Y, Ono Y, Kojima A, Kimura Y, Komori T, et al. fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. Nuc Acids Res. 2007; 35:145–8.

Article
Google Scholar

Bloom JD, Arnold FH. In the light of directed evolution: Pathways of adaptive protein evolution. Proc Natl Acad Sci USA. 2009; 106:9995–10000.

Article
CAS
PubMed
PubMed Central
Google Scholar

Salverda MLM, Dellus E, Gorter FA, Debets AJM, van der Oost J, Hoekstra RF, Tawfik DS, de Visser JAGM. Initial mutations direct alternative pathways of protein evolution. PLoS Genet. 2011; 7:1001321.

Article
Google Scholar

Cabanillas L, Arribas M, Lázaro E. Evolution at increased error rate leads to the coexistence of multiple adaptive pathways in an rna virus. BMC Evol Biol. 2013; 13:11.

Article
CAS
PubMed
PubMed Central
Google Scholar

Lobkovsky AE, Wolf YI, Koonin EV. Predictability of evolutionary trajectories in fitness landscapes. PLoS Comp Biol. 2011; 7:1002302.

Article
Google Scholar

Lobkovsky AE, Wolf YI, Koonin EV. Quantifying the similarity of monotonic trajectories in rough and smooth fitness landscapes. Mol Biosyst. 2013; 9:1627.

Article
CAS
PubMed
PubMed Central
Google Scholar

Aguirre J, Manrubia S. Tipping points and early warning signals in the genomic composition of populations induced by environmental changes. Sci Rep. 2015; 5:9664.

Article
CAS
PubMed
PubMed Central
Google Scholar